brukerconverter - npm Package Compare versions

Comparing version 6.0.5 to 6.0.6-pre.1675950152

lib/index.js

@@ -21,2 +21,3 @@ 'use strict';
  */
+
 function groupByExperiments(fileCollection, options = {}) {
@@ -42,9 +43,13 @@ let {
     if (file.relativePath.match(/\/pdata\/[0-9]+\/.*$/)) {
-      currentProcessingNo = Number(parts[parts.length - 2]);
-      currentExperimentNo = Number(parts[parts.length - 4]);
-      name = parts[parts.length - 5];
+      const pdataIndex = parts.indexOf('pdata');
+      currentProcessingNo = Number(parts[pdataIndex + 1]);
+      const expno = parseInt(parts[pdataIndex - 1], 10);
+      currentExperimentNo = isNaN(expno) ? 0 : expno;
+      name = parts[pdataIndex - 2] || parts[pdataIndex - 1];
       id = parts.slice(0, -3).join('/');
-    } else if (file.relativePath.match(/[0-9]+\/.*$/)) {
-      currentExperimentNo = Number(parts[parts.length - 2]);
-      name = parts[parts.length - 3] || parts[parts.length - 2];
+    } else if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
+      const firstLevel = parts.indexOf(file.name);
+      const expno = parseInt(parts[firstLevel - 1], 10);
+      currentExperimentNo = isNaN(expno) ? 0 : expno;
+      name = parts[firstLevel - 2] || parts[firstLevel - 1];
       id = parts.slice(0, -1).join('/');
@@ -78,3 +83,3 @@ } else {
       const processedData = experiment.processedData[currentProcessingNo];
-      processedData.fileCollectionItems.push(file);
+      processedData.fileCollectionItems.push(file); // check if it can be moved into the conditional block
       if (file.name.match(/^(1r|1i|2rr|procs|proc2s)$/)) {
@@ -92,3 +97,3 @@ processedData[file.name] = file;
     } else {
-      experiment.fileCollectionItems.push(file);
+      experiment.fileCollectionItems.push(file); // check if it can be moved into the conditional block
       if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
@@ -137,5 +142,3 @@ experiment[file.name] = file;
   for (let key in experiments) {
-    const experiment = { ...experiments[key] };
-    const processed = experiment.processedData;
-    delete experiment.processedData;
+    const { processedData: processed, ...experiment } = { ...experiments[key] };
     if (experiment.ser || experiment.fid) {
@@ -145,7 +148,7 @@ if (Object.keys(processed).length > 0) {
         if (firstProcessed.procs) {
-          experiment.fileCollectionItems.push(firstProcessed.procs);
+          experiment.fileCollectionItems.push(firstProcessed.procs); //seems useless
           experiment.procs = firstProcessed.procs;
         }
         if (firstProcessed.proc2s) {
-          experiment.fileCollectionItems.push(firstProcessed.proc2s);
+          // experiment.fileCollectionItems.push(firstProcessed.proc2s); //seems useless
           experiment.proc2s = firstProcessed.proc2s;
@@ -240,5 +243,6 @@ }
 
-  const SW_H = Number(spectra.meta.SW_h[0]);
+  const SW_H = parseFloat(spectra.meta.SW_h[0]);
 
-  const SF = Number(spectra.meta.SFO1[0]);
+  const SF = parseFloat(spectra.meta.SFO1[0]);
+  const dtypa = parseInt(spectra.meta.DTYPA, 10);
 
@@ -291,11 +295,11 @@ spectra.meta.DATATYPE = 'NMR FID';
 
-    // const dtypa = spectra.meta.DTYPA;// we should use it for float or double FID data;
+    const method = dtypa === 2 ? 'readFloat64' : 'readInt32';
     if (aqMode === QSEQ) {
       for (let i = 0; i < nbPoints; i++) {
-        spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
+        spectra.spectra[j].data.re[i] = ioBuffer[method]();
       }
     } else {
       for (let i = 0; i < nbPoints; i++) {
-        spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
-        spectra.spectra[j].data.im[i] = ioBuffer.readInt32();
+        spectra.spectra[j].data.re[i] = ioBuffer[method]();
+        spectra.spectra[j].data.im[i] = ioBuffer[method]();
       }
@@ -302,0 +306,0 @@ }

package.json

 {
   "name": "brukerconverter",
-  "version": "6.0.5",
+  "version": "6.0.6-pre.1675950152",
   "description": "Parse and convert Bruker raw data",
@@ -53,2 +53,2 @@ "main": "lib/index.js",
   }
-}
+}

src/__tests__/convertFileList.test.js

 import { getCoffee } from 'bruker-data-test';
+import { fileCollectionFromPath } from 'filelist-utils';
 import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 
 import { convertFileCollection } from '../convertFileCollection.js';
+import { join } from 'path';
 
@@ -10,2 +12,26 @@ expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
 describe('convertFileCollection', () => {
+  it('convert folder without expno level', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/withoutExpno'),
+    );
+    const results = await convertFileCollection(fileCollection, {
+      converter: { keepFiles: true },
+    });
+
+    expect(results[0].source).toMatchCloseTo({
+      name: 'withoutExpno',
+      expno: 0,
+      is1D: true,
+      isFID: true,
+    });
+    expect(results[1].source).toMatchCloseTo({
+      name: 'withoutExpno',
+      expno: 0,
+      procno: 1,
+      is1D: true,
+      isFT: true,
+    });
+    expect(results[1].spectra[0].data.re).toHaveLength(65536 / 2);
+    expect(results[0].spectra[0].data.re).toHaveLength(65536 / 2);
+  });
   it('advanced example', async () => {
@@ -12,0 +38,0 @@ const fileCollection = await getCoffee();

src/__tests__/groupByExperiments.test.js

 import { getCoffee } from 'bruker-data-test';
+import { fileCollectionFromPath } from 'filelist-utils';
+import { join } from 'path';
 
 import { groupByExperiments } from '../groupByExperiments.js';
 
+describe('groupByExperiment without expno', () => {
+  it('processed data and raw 1D data', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/withoutExpno'),
+    );
+    const results = groupByExperiments(fileCollection);
+    expect(results).toHaveLength(2);
+    expect(results[0].expno).toBe(0);
+    expect(results[0].name).toBe('withoutExpno');
+    expect(results[1].expno).toBe(0);
+    expect(results[1].name).toBe('withoutExpno');
+  });
+});
 describe('groupByExperiments', () => {
@@ -6,0 +21,0 @@ it('no options', async () => {

src/groupByExperiments.js

@@ -13,2 +13,3 @@ /**
  */
+
 export function groupByExperiments(fileCollection, options = {}) {
@@ -34,9 +35,13 @@ let {
     if (file.relativePath.match(/\/pdata\/[0-9]+\/.*$/)) {
-      currentProcessingNo = Number(parts[parts.length - 2]);
-      currentExperimentNo = Number(parts[parts.length - 4]);
-      name = parts[parts.length - 5];
+      const pdataIndex = parts.indexOf('pdata');
+      currentProcessingNo = Number(parts[pdataIndex + 1]);
+      const expno = parseInt(parts[pdataIndex - 1], 10);
+      currentExperimentNo = isNaN(expno) ? 0 : expno;
+      name = parts[pdataIndex - 2] || parts[pdataIndex - 1];
       id = parts.slice(0, -3).join('/');
-    } else if (file.relativePath.match(/[0-9]+\/.*$/)) {
-      currentExperimentNo = Number(parts[parts.length - 2]);
-      name = parts[parts.length - 3] || parts[parts.length - 2];
+    } else if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
+      const firstLevel = parts.indexOf(file.name);
+      const expno = parseInt(parts[firstLevel - 1], 10);
+      currentExperimentNo = isNaN(expno) ? 0 : expno;
+      name = parts[firstLevel - 2] || parts[firstLevel - 1];
       id = parts.slice(0, -1).join('/');
@@ -70,3 +75,3 @@ } else {
       const processedData = experiment.processedData[currentProcessingNo];
-      processedData.fileCollectionItems.push(file);
+      processedData.fileCollectionItems.push(file); // check if it can be moved into the conditional block
       if (file.name.match(/^(1r|1i|2rr|procs|proc2s)$/)) {
@@ -84,3 +89,3 @@ processedData[file.name] = file;
     } else {
-      experiment.fileCollectionItems.push(file);
+      experiment.fileCollectionItems.push(file); // check if it can be moved into the conditional block
       if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
@@ -129,5 +134,3 @@ experiment[file.name] = file;
   for (let key in experiments) {
-    const experiment = { ...experiments[key] };
-    const processed = experiment.processedData;
-    delete experiment.processedData;
+    const { processedData: processed, ...experiment } = { ...experiments[key] };
     if (experiment.ser || experiment.fid) {
@@ -137,7 +140,7 @@ if (Object.keys(processed).length > 0) {
         if (firstProcessed.procs) {
-          experiment.fileCollectionItems.push(firstProcessed.procs);
+          experiment.fileCollectionItems.push(firstProcessed.procs); //seems useless
           experiment.procs = firstProcessed.procs;
         }
         if (firstProcessed.proc2s) {
-          experiment.fileCollectionItems.push(firstProcessed.proc2s);
+          // experiment.fileCollectionItems.push(firstProcessed.proc2s); //seems useless
           experiment.proc2s = firstProcessed.proc2s;
@@ -144,0 +147,0 @@ }

src/util/setFIDSpectrumData.js

@@ -16,5 +16,6 @@ import { IOBuffer } from 'iobuffer';
 
-  const SW_H = Number(spectra.meta.SW_h[0]);
+  const SW_H = parseFloat(spectra.meta.SW_h[0]);
 
-  const SF = Number(spectra.meta.SFO1[0]);
+  const SF = parseFloat(spectra.meta.SFO1[0]);
+  const dtypa = parseInt(spectra.meta.DTYPA, 10);
 
@@ -67,11 +68,11 @@ spectra.meta.DATATYPE = 'NMR FID';
 
-    // const dtypa = spectra.meta.DTYPA;// we should use it for float or double FID data;
+    const method = dtypa === 2 ? 'readFloat64' : 'readInt32';
     if (aqMode === aqModeDirect.QSEQ) {
       for (let i = 0; i < nbPoints; i++) {
-        spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
+        spectra.spectra[j].data.re[i] = ioBuffer[method]();
       }
     } else {
       for (let i = 0; i < nbPoints; i++) {
-        spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
-        spectra.spectra[j].data.im[i] = ioBuffer.readInt32();
+        spectra.spectra[j].data.re[i] = ioBuffer[method]();
+        spectra.spectra[j].data.im[i] = ioBuffer[method]();
       }
@@ -78,0 +79,0 @@ }

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Improved metrics

Total package byte prevSize

603494

increased by1012.99%

Number of package files

30

increased by30.43%

Lines of code

1599

increased by2.96%

Worsened metrics

Number of low quality alerts

2

increased by100%

Number of medium supply chain risk alerts

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No dependency changes